bigwig

Calculate genome coverage for fragments and write result to bigWig file.

Usage and options

scatac_fragment_tools bigwig -i <FRAGMENTS_FILENAME> -c <CHROM_SIZES_FILENAME> -o <BIGWIG_FILENAME>

Required arguments

-c, –chrom

Filename with chromosome sizes (*.chrom.sizes, *.fa.fai).

-i, –frag

Fragments TSV file for which to calculate genome coverage.

-o, –bw

BigWig filename to which the genome coverage data will be written.

Optional arguments

-n, –normalize

Normalize genome coverage data by dividing by sequencing depth (number of fragments) multiplied by 1 million. Default: False

-s, –scaling

Scaling factor for genome coverage data. If normalization is enabled, scaling is applied afterwards. Default: 1.0

-x, –cut-sites

Use 1 bp Tn5 cut sites (start and end of each fragment) instead of whole fragment length for coverage calculation. Default: False

–chrom-prefix

Add chromosome prefix to each chromosome name found in the fragments file. Default: False